Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:ARAP3-CTBP2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ARAP3-CTBP2
	FusionPDB ID: 5773
	FusionGDB2.0 ID: 5773
		Hgene	Tgene
	Gene symbol	ARAP3	CTBP2
	Gene ID	64411	1488
	Gene name	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	C-terminal binding protein 2
	Synonyms	CENTD3\|DRAG1	-
	Cytomap	5q31.3	10q26.13
	Type of gene	protein-coding	protein-coding
	Description	arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3ARF-GAP, RHO-GAP, ankyrin repeat and plekstrin homology domains-containing protein 3Arf and Rho GAP adapter protein 3PtdIns(3,4,5)P3-binding proteincentaurin-delta-3phosphoinos	C-terminal-binding protein 2ribeye
	Modification date	20200327	20200313
	UniProtAcc	Q8WWN8 Main function of 5'-partner protein: FUNCTION: Phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating protein that modulates actin cytoskeleton remodeling by regulating ARF and RHO family members. Is activated by phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) binding. Can be activated by phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding, albeit with lower efficiency. Acts on ARF6, RAC1, RHOA and CDC42. Plays a role in the internalization of anthrax toxin. {ECO:0000269\|PubMed:11804589, ECO:0000269\|PubMed:15569923}.	P56545 Main function of 5'-partner protein: FUNCTION: Corepressor targeting diverse transcription regulators. Functions in brown adipose tissue (BAT) differentiation (By similarity). {ECO:0000250}.; FUNCTION: Isoform 2 probably acts as a scaffold for specialized synapses.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000239440, ENST00000508305, ENST00000513878, ENST00000512390,	ENST00000309035, ENST00000334808, ENST00000476817, ENST00000337195, ENST00000411419, ENST00000494626, ENST00000531469,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 3=27	11 X 9 X 4=396
	# samples	3	13
	** MAII score	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(13/396*10)=-1.60698880705116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ARAP3 [Title/Abstract] AND CTBP2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ARAP3 [Title/Abstract] AND CTBP2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ARAP3(141045991)-CTBP2(126678267), # samples:2
Anticipated loss of major functional domain due to fusion event.	ARAP3-CTBP2 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. ARAP3-CTBP2 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. ARAP3-CTBP2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. ARAP3-CTBP2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. ARAP3-CTBP2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. ARAP3-CTBP2 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. ARAP3-CTBP2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:141045991/chr10:126678267)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.

Retention analysis results of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features, are available here.

Fusion gene breakpoints across ARAP3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across CTBP2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000508305	ARAP3	chr5	141045991	-	ENST00000337195	CTBP2	chr10	126678267	-	4375	2528	34	2610	858
ENST00000508305	ARAP3	chr5	141045991	-	ENST00000531469	CTBP2	chr10	126678267	-	3002	2528	34	2610	858
ENST00000508305	ARAP3	chr5	141045991	-	ENST00000411419	CTBP2	chr10	126678267	-	3002	2528	34	2610	858
ENST00000239440	ARAP3	chr5	141045991	-	ENST00000494626	CTBP2	chr10	126678267	-	3112	2638	66	2720	884
ENST00000513878	ARAP3	chr5	141045991	-	ENST00000337195	CTBP2	chr10	126678267	-	3474	1627	54	1709	551
ENST00000513878	ARAP3	chr5	141045991	-	ENST00000531469	CTBP2	chr10	126678267	-	2101	1627	54	1709	551
ENST00000513878	ARAP3	chr5	141045991	-	ENST00000411419	CTBP2	chr10	126678267	-	2101	1627	54	1709	551

DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000508305	ENST00000337195	ARAP3	chr5	141045991	-	CTBP2	chr10	126678267	-	0.004115798	0.9958841
ENST00000508305	ENST00000531469	ARAP3	chr5	141045991	-	CTBP2	chr10	126678267	-	0.015352499	0.9846475
ENST00000508305	ENST00000411419	ARAP3	chr5	141045991	-	CTBP2	chr10	126678267	-	0.015352499	0.9846475
ENST00000239440	ENST00000494626	ARAP3	chr5	141045991	-	CTBP2	chr10	126678267	-	0.014228651	0.9857714
ENST00000513878	ENST00000337195	ARAP3	chr5	141045991	-	CTBP2	chr10	126678267	-	0.05559494	0.9444051
ENST00000513878	ENST00000531469	ARAP3	chr5	141045991	-	CTBP2	chr10	126678267	-	0.20850664	0.7914934
ENST00000513878	ENST00000411419	ARAP3	chr5	141045991	-	CTBP2	chr10	126678267	-	0.20850664	0.7914934

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

Top

Fusion Protein Breakpoint Sequences for ARAP3-CTBP2

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
ARAP3	chr5	141045991	CTBP2	chr10	126678267	1627	525	EDMVHLRRLQEINIRQASWVWLQEDF
ARAP3	chr5	141045991	CTBP2	chr10	126678267	2528	832	EDMVHLRRLQEINIRQASWVWLQEDF
ARAP3	chr5	141045991	CTBP2	chr10	126678267	2638	858	EDMVHLRRLQEINIRQASWVWLQEDF

Top

Potential FusionNeoAntigen Information of ARAP3-CTBP2 in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

ARAP3-CTBP2_141045991_126678267.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B45:01	QEINIRQA	0.9997	0.9287	9	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B50:02	QEINIRQA	0.9997	0.723	9	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B41:01	QEINIRQA	0.9955	0.9824	9	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B50:01	QEINIRQA	0.9717	0.8439	9	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B27:05	RRLQEINIR	0.9994	0.8919	6	15
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B27:04	RRLQEINIR	0.9985	0.763	6	15
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B45:01	QEINIRQAS	0.99	0.9641	9	18
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B57:01	NIRQASWVW	0.9832	0.994	12	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B50:02	QEINIRQAS	0.9811	0.7266	9	18
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-A32:13	NIRQASWVW	0.7873	0.9979	12	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-A32:13	EINIRQASW	0.6096	0.9783	10	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B41:01	QEINIRQAS	0.5487	0.9691	9	18
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B50:01	QEINIRQAS	0.3199	0.8005	9	18
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:02	QEINIRQASW	0.9998	0.8575	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:03	QEINIRQASW	0.9998	0.9952	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B57:01	INIRQASWVW	0.9997	0.9948	11	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:05	QEINIRQASW	0.9992	0.947	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:02	LQEINIRQASW	0.9907	0.963	8	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:03	LQEINIRQASW	0.9898	0.9973	8	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:02	QEINIRQASWV	0.984	0.9297	9	20
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:03	QEINIRQASWV	0.9809	0.9954	9	20
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B40:06	QEINIRQA	0.9999	0.7558	9	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B27:14	RRLQEINIR	0.9993	0.8253	6	15
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B40:06	QEINIRQAS	0.9809	0.7574	9	18
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B27:03	RRLQEINIR	0.9719	0.9031	6	15
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:04	QEINIRQASW	0.9997	0.6435	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:08	QEINIRQASW	0.9996	0.9253	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:09	QEINIRQASW	0.9996	0.9283	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B27:14	RRLQEINIRQ	0.9994	0.6868	6	16
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B40:03	QEINIRQASW	0.998	0.8657	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:10	QEINIRQASW	0.9527	0.8873	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B27:14	RRLQEINIRQA	1	0.6621	6	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B50:05	QEINIRQA	0.9717	0.8439	9	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B50:04	QEINIRQA	0.9717	0.8439	9	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B27:08	RRLQEINIR	0.9994	0.7919	6	15
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B27:10	RRLQEINIR	0.999	0.8923	6	15
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B57:10	NIRQASWVW	0.9832	0.994	12	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-A25:01	EINIRQASW	0.9509	0.9721	10	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B15:13	NIRQASWVW	0.9336	0.7737	12	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-A32:01	NIRQASWVW	0.8486	0.9953	12	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B15:13	EINIRQASW	0.8435	0.7112	10	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-A25:01	NIRQASWVW	0.7228	0.9706	12	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B53:02	NIRQASWVW	0.7149	0.8626	12	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B50:04	QEINIRQAS	0.3199	0.8005	9	18
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B50:05	QEINIRQAS	0.3199	0.8005	9	18
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:22	QEINIRQASW	0.9998	0.8575	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:13	QEINIRQASW	0.9998	0.9952	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:07	QEINIRQASW	0.9998	0.9952	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:26	QEINIRQASW	0.9998	0.9952	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B57:10	INIRQASWVW	0.9997	0.9948	11	21
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:21	QEINIRQASW	0.9996	0.5969	9	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:22	LQEINIRQASW	0.9907	0.963	8	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:07	LQEINIRQASW	0.9898	0.9973	8	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:26	LQEINIRQASW	0.9898	0.9973	8	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:13	LQEINIRQASW	0.9898	0.9973	8	19
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:22	QEINIRQASWV	0.984	0.9297	9	20
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:13	QEINIRQASWV	0.9809	0.9954	9	20
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:26	QEINIRQASWV	0.9809	0.9954	9	20
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:07	QEINIRQASWV	0.9809	0.9954	9	20
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	HLA-B44:21	QEINIRQASWV	0.9734	0.7355	9	20

Top

Potential FusionNeoAntigen Information of ARAP3-CTBP2 in HLA II

ARAP3-CTBP2_141045991_126678267.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	DRB1-1203	MVHLRRLQEINIRQA	2	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	DRB1-1219	MVHLRRLQEINIRQA	2	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	DRB1-1220	MVHLRRLQEINIRQA	2	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	DRB1-1503	MVHLRRLQEINIRQA	2	17
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2638	DRB1-1523	MVHLRRLQEINIRQA	2	17

Top

Fusion breakpoint peptide structures of ARAP3-CTBP2

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
8175	RRLQEINIRQASWV	ARAP3	CTBP2	chr5	141045991	chr10	126678267	2638

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ARAP3-CTBP2

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	8175	RRLQEINIRQASWV	-7.15543	-7.26883
HLA-B14:02	3BVN	8175	RRLQEINIRQASWV	-4.77435	-5.80965
HLA-B52:01	3W39	8175	RRLQEINIRQASWV	-6.80875	-6.92215
HLA-B52:01	3W39	8175	RRLQEINIRQASWV	-4.20386	-5.23916
HLA-A11:01	4UQ2	8175	RRLQEINIRQASWV	-7.5194	-8.5547
HLA-A11:01	4UQ2	8175	RRLQEINIRQASWV	-6.9601	-7.0735
HLA-A24:02	5HGA	8175	RRLQEINIRQASWV	-7.52403	-7.63743
HLA-A24:02	5HGA	8175	RRLQEINIRQASWV	-5.82433	-6.85963
HLA-B27:05	6PYJ	8175	RRLQEINIRQASWV	-3.28285	-4.31815
HLA-B44:05	3DX8	8175	RRLQEINIRQASWV	-5.91172	-6.94702
HLA-B44:05	3DX8	8175	RRLQEINIRQASWV	-4.24346	-4.35686

Top

Vaccine Design for the FusionNeoAntigens of ARAP3-CTBP2

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
ARAP3-CTBP2	chr5	141045991	chr10	126678267	10	19	EINIRQASW	AGGAGATCAATATCCGCCAGGCATCGT
ARAP3-CTBP2	chr5	141045991	chr10	126678267	11	21	INIRQASWVW	AGATCAATATCCGCCAGGCATCGTGGGTGT
ARAP3-CTBP2	chr5	141045991	chr10	126678267	12	21	NIRQASWVW	TCAATATCCGCCAGGCATCGTGGGTGT
ARAP3-CTBP2	chr5	141045991	chr10	126678267	6	15	RRLQEINIR	TGCGGCGGCTACAGGAGATCAATATCC
ARAP3-CTBP2	chr5	141045991	chr10	126678267	6	16	RRLQEINIRQ	TGCGGCGGCTACAGGAGATCAATATCCGCC
ARAP3-CTBP2	chr5	141045991	chr10	126678267	6	17	RRLQEINIRQA	TGCGGCGGCTACAGGAGATCAATATCCGCCAGG
ARAP3-CTBP2	chr5	141045991	chr10	126678267	8	19	LQEINIRQASW	GGCTACAGGAGATCAATATCCGCCAGGCATCGT
ARAP3-CTBP2	chr5	141045991	chr10	126678267	9	17	QEINIRQA	TACAGGAGATCAATATCCGCCAGG
ARAP3-CTBP2	chr5	141045991	chr10	126678267	9	18	QEINIRQAS	TACAGGAGATCAATATCCGCCAGGCAT
ARAP3-CTBP2	chr5	141045991	chr10	126678267	9	19	QEINIRQASW	TACAGGAGATCAATATCCGCCAGGCATCGT
ARAP3-CTBP2	chr5	141045991	chr10	126678267	9	20	QEINIRQASWV	TACAGGAGATCAATATCCGCCAGGCATCGTGGG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
ARAP3-CTBP2	chr5	141045991	chr10	126678267	2	17	MVHLRRLQEINIRQA	ACATGGTGCATCTGCGGCGGCTACAGGAGATCAATATCCGCCAGG

Top

Information of the samples that have these potential fusion neoantigens of ARAP3-CTBP2

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
UCEC	ARAP3-CTBP2	chr5	141045991	ENST00000239440	chr10	126678267	ENST00000494626	TCGA-AP-A5FX-01A

Top

Potential target of CAR-T therapy development for ARAP3-CTBP2

Predicted 3D structure. We used RoseTTAFold.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

Top

Related Drugs to ARAP3-CTBP2

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to ARAP3-CTBP2

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)